Contacts of the helix formed by residues 231 - 242 (chain A) in PDB entry 2OZO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ILE 4.5 4.5 + - - +
154A ALA* 4.1 26.0 - - - +
156A THR 5.2 8.5 - - - +
158A HIS* 6.2 1.6 - - - -
221A TYR* 3.7 13.5 - - + -
229A PHE* 3.4 9.0 - - - +
230A ASP* 1.3 83.5 - - + +
232A LEU* 1.3 65.6 + - - +
233A TRP* 3.7 8.7 + - - +
234A GLN* 2.7 43.8 + - - +
235A LEU* 3.4 14.2 + - - +
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS* 3.7 41.5 + - + +
163A TRP* 4.1 13.0 - - + -
164A TYR* 4.9 2.7 - - + -
189A LEU* 4.1 20.9 - - + -
198A TYR* 4.2 20.9 - - + -
213A ILE* 4.2 8.1 - - + -
221A TYR* 3.3 43.2 - - + -
231A THR* 1.3 73.8 - - - +
233A TRP* 1.3 53.4 + - - +
235A LEU* 2.9 19.7 + - + +
236A VAL* 2.6 38.4 + - - +
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Residues in contact with TRP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A MET* 4.8 11.7 - - + -
126A TYR* 3.6 30.1 - + + -
129A GLN* 4.8 13.0 - - - -
153A ILE* 3.8 35.2 - - + -
156A THR* 3.2 35.9 - - + +
158A HIS* 5.2 3.6 - - + +
161A MET* 3.1 42.1 - - + +
163A TRP* 4.0 18.9 - + + -
231A THR* 3.3 9.5 - - - +
232A LEU* 1.3 77.8 - - - +
234A GLN* 1.3 56.7 + - + +
236A VAL* 3.3 1.4 + - + +
237A GLU* 2.8 54.2 + - + +
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Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.0 36.3 - - + +
118A LEU* 3.7 6.2 - - + +
122A MET* 4.1 32.3 - - + +
153A ILE* 5.3 9.3 - - + +
154A ALA* 5.2 7.2 - - - +
229A PHE* 4.1 3.8 - - + -
230A ASP* 3.0 20.7 - - - +
231A THR* 2.7 50.3 + - - +
232A LEU 3.2 0.2 - - - -
233A TRP* 1.3 72.6 - - + +
235A LEU* 1.3 56.0 + - - +
237A GLU 3.2 0.3 + - - -
238A TYR* 2.7 36.0 + - - +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 5.6 1.3 - - + -
213A ILE* 3.8 38.8 - - + -
221A TYR* 4.2 7.0 - - + -
223A ILE* 3.2 29.2 - - + -
229A PHE* 3.3 34.0 - - + -
231A THR 3.4 8.1 + - - +
232A LEU* 2.9 24.4 + - + +
234A GLN* 1.3 79.5 - - - +
236A VAL* 1.3 56.2 + - + +
238A TYR* 3.2 2.1 + - - +
239A LEU* 2.9 44.9 + - + +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 3.8 35.9 - - + +
187A PHE* 3.9 29.2 - - + -
189A LEU* 4.2 23.8 - - + -
232A LEU 2.6 19.9 + - - +
233A TRP* 3.5 7.9 - - + +
235A LEU* 1.3 76.1 - - + +
237A GLU* 1.3 66.1 + - - +
239A LEU* 3.2 2.9 + - + -
240A LYS* 3.0 30.4 + - - +
250A LEU* 3.8 13.9 - - + +
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.6 20.4 - - + +
122A MET* 3.9 17.4 - - + +
163A TRP* 5.3 1.0 + - - -
233A TRP* 2.8 48.0 + - + +
234A GLN 3.9 1.3 - - - +
236A VAL* 1.3 73.7 - - - +
238A TYR* 1.3 60.7 + - - +
240A LYS* 2.9 58.8 + - - +
241A LEU* 3.5 10.7 + - - +
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.6 31.5 - - + +
115A PHE* 4.0 22.7 - + - -
118A LEU* 3.7 14.3 - - + +
223A ILE* 4.6 1.8 - - + -
227A THR* 4.5 10.1 + - + +
229A PHE* 3.2 30.5 - + + -
234A GLN 2.7 18.3 + - - +
235A LEU 3.3 4.0 - - - +
236A VAL 3.1 0.2 - - - -
237A GLU* 1.3 77.8 - - - +
239A LEU* 1.3 67.2 + - + +
241A LEU* 3.0 8.4 + - + +
242A LYS* 2.9 51.7 + - + +
244A ASP* 2.9 36.8 + - - -
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.3 11.4 - - + -
213A ILE* 6.2 0.9 - - + -
223A ILE* 4.4 10.8 - - + -
235A LEU* 2.9 40.6 + - + +
236A VAL* 5.1 0.7 - - + -
238A TYR* 1.3 83.0 - - + +
240A LYS* 1.3 59.8 + - - +
241A LEU 3.2 0.4 + - - -
242A LYS 3.1 19.6 - - - +
243A ALA* 4.4 1.3 - - - +
244A ASP* 3.8 19.7 - - - +
246A LEU* 3.6 31.0 - - + -
249A CYS* 3.6 7.8 - - - -
250A LEU* 3.2 45.7 + - + +
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TRP* 5.3 4.0 - - - +
187A PHE* 4.4 7.9 - - + -
236A VAL* 3.0 21.0 + - - +
237A GLU* 2.9 55.9 + - - +
238A TYR 3.0 0.2 - - - -
239A LEU* 1.3 78.4 - - - +
241A LEU* 1.3 64.7 + - + +
249A CYS* 3.7 11.3 - - - +
250A LEU* 3.8 29.7 - - + +
251A LYS* 4.1 18.0 + - - +
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 5.5 11.4 - - + -
117A CYS* 5.5 7.0 - - + -
118A LEU* 4.9 24.2 - - + +
121A ALA* 5.6 7.2 - - + -
237A GLU 3.9 11.2 - - - +
238A TYR* 3.0 5.4 + - + +
240A LYS* 1.3 90.3 - - + +
242A LYS* 1.3 68.3 + - + +
243A ALA 4.0 0.3 + - - -
249A CYS* 3.2 15.7 - - - -
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Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 5.1 15.5 - - + -
238A TYR* 2.9 43.5 + - + +
239A LEU* 3.1 28.0 - - - +
241A LEU* 1.3 80.8 + - + +
243A ALA* 1.3 63.3 - - - +
244A ASP* 3.6 11.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il